Best Practices for Exporting Files??

I'm new to Premiere (coming from FCP).  I used Premiere months ago to compress some ProRes files to h.264 files for the web.  I sent the files through Media Encoder and everything seemed fine.  However, I realized after several weeks that the audio in all of the files was a few frames out of sync.  Having not been a Premiere user at the time I did not do much research and decided to just use MPEG Streamclip from then on.
Now that I'm learning how to use Premiere, I looked up the issue on the forums and found that many people have had similar issues with the audio being out of sync after exporting. However, there are tons of different scenerios in which it seems to be occuring.  The one common variable that I've noticed (among many of the threads, but not all) is that many of the people are exporting to a Quicktime format. 
While I don't remember all the details of my export and sequence settings from my issue months ago (so I don't want to address that specific case), I am curious as to what are some "Best Practices" when exporting from Premiere Pro? Is there any advantage/disadvantage to use AME rather than exporting directly from Premiere Pro? In general, I will just be exporting as H.264 files for the web, MPEG-2 for DVD, and ProRes 422 for After Effects (or sometimes to bring into MPEG Streamclip). 
I shoot almost entirely in AVCHD, and usually at 1080p 30fps.  I'm running CS5 on a Macbook Pro 15" 2.0 Quad Core i7 8GB RAM.
While the question may seem broad, my main concern that I want to avoid is having the audio out of sync.  But also I just want to know of any important details to keep in mind to prevent other issues.
Thanks,
Mike

> I'm running CS5...
What specific version? We're up to 5.0.4 now.
There have been bug fixes for audio/video synch in the updates. One of the fixes was for a bug in the conforming of audio and indexing of MPEG files, so you need to delete your media cache files and let Premiere Pro create new ones for this fix to take effect.

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